MolNFT v1 · #140329 · protein
Crystal structure of catalytic domain of uggt (udp-bound form) from thermomyces dupontii
5Y7F: “Crystal structure of catalytic domain of uggt (udp-bound form) from thermomyces dupontii”. X-ray diffraction, 2 ligands (UDP, CA), 2 pockets (best druggability 0.70). MolNFT v1 #140329 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5Y7F
- Type
- protein
- Length
- 267 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uggt
- Ligands
- UDP, CA
- Pockets
- 2 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uggt | protein | 267 | 45% helix, 16% strand | — |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · chains A
- CA · Calcium ion · metal · chains A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 308 | 0.70 | 0.84 | 34 | UDP, TRS, CA |
| 2 | 57 | 0.29 | 0.74 | 12 | empty |
Modifications
Observed in the structure: 10 modified, 2 disulfide (engineered, disulfide).
Compared structures
- 5Y7F · Crystal structure of catalytic domain of UGGT (UDP-bound form) from Thermomyces dupontii · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 5Y7F · PDBe 5Y7F
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